Thank you Justin and Peter for your responses. I tried extending the time
on the npt equilibration. It helped but not much. My final pressure after
the MD run was about 1.15 bar compared to ref_p which was set to 1 bar.
Peter, I will try to analyze the potential error using RMSD and Drift.
Than
So your density graph looks stabilized? I also tend to look for changes in
box x, y, z as well since the scale of their changes is easier to track.
Sometimes it helps to look at the error vs. rmsd vs total drift statistics as
well for such parameters that are easier to track - again if density sh
Hi,
I'm still in my first few months of using Gromacs. I started by
creating an *.itp and *.top file for Ethanol using CHARMM force field
parameters. I made the molecule and it looked fine, put 1000
molecules in a box, energy minimized it to a negative potential
energy, viewed it on VMD, again l
Fabian Casteblanco wrote:
Hi,
I'm still in my first few months of using Gromacs. I started by
creating an *.itp and *.top file for /Ethanol/ using CHARMM force field
parameters. I made the molecule and it looked fine, put 1000 molecules
in a box, energy minimized it to a negative potenti
Hi,
I'm still in my first few months of using Gromacs. I started by creating an
*.itp and *.top file for *Ethanol* using CHARMM force field parameters. I
made the molecule and it looked fine, put 1000 molecules in a box, energy
minimized it to a negative potential energy, viewed it on VMD, again
bject: Re: [gmx-users] Pressure Coupling Problem
I finally figured it out. I went through every parameter step by step and it
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs
would have given me a warning (hint hint). That explains why my P.E. was 10^-5
instead of
I finally figured it out. I went through every parameter step by step and it
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs
would have given me a warning (hint hint). That explains why my P.E. was
10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most
o
Alright, sorry that I wasn't able to help. I'm confused by some
apparent contradictions in your posts and I'm not sure that I'm going
to be useful to you here.
Quoting
http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: "No
matter how much minimization I do the volume of th
Nope not an A/nm problem.
As a simple test I take spc.gro from share/top.
I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
water_center.
I then solvate with genbox, minimize and run using the mdp file I provided
earlier.
No matter how much minimization I do the volume of the
So your problem with the small water box was solved simply by adding more
minimization? I then suspect that all of your problems are simply related to a
bad starting structure -- and by the sound of it is really is very bad. Are you
sure that you don't have an angstrom / nm problem here?
Chris
On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> So I got my small water box (800 waters) to behave stably with pressure
>> coupling after more minimization but I still can't get my large system to
>> work with pressure coupling. I tried minimizing but I can never
Joe Joe wrote:
So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system
to work with pressure coupling. I tried minimizing but I can never get
the Fmax to be less 10^2, which is pretty normal for protein/wat
So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system to
work with pressure coupling. I tried minimizing but I can never get the Fmax
to be less 10^2, which is pretty normal for protein/water simulations of
lar
On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz wrote:
>
>
> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe wrote:
>
>> HI Chris,
>>
>> On Tue, Apr 7, 2009 at 9:31 PM, wrote:
>>
>>> Hi Ilya,
>>>
>>> First thing that comes to mind is that it is strange to couple a
>>> coulombic switching function with P
I tried .1, and 10 ps tau_p values. I guess I can try smaller values.
On Wed, Apr 8, 2009 at 10:44 AM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> Hi Chris,
>>
>> When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
>> set up the correct constraints. I've tested it a
Yeah I only gave a partial. Tried to remove the QM params. I do use
constraints = all-bonds.
On Wed, Apr 8, 2009 at 9:18 AM, wrote:
> You say "I run all he sims with constraints=all-bonds", but I don't see
> that in the mdp options that you provided. I even put your text in a file
> and grepped
On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe wrote:
> HI Chris,
>
> On Tue, Apr 7, 2009 at 9:31 PM, wrote:
>
>> Hi Ilya,
>>
>> First thing that comes to mind is that it is strange to couple a coulombic
>> switching function with PME. While this could possibly be done correctly, I
>> doubt that it is
Joe Joe wrote:
Hi Chris,
When I create the topology for the 4fs timestep I use pdb2gmx -vsite h.
I set up the correct constraints. I've tested it and it conserves energy
in NVE. I run all he sims with constraints=all-bonds. I am now running a
single water box (800 water molecules) with 1s t
You say "I run all he sims with constraints=all-bonds", but I don't
see that in the mdp options that you provided. I even put your text in
a file and grepped for it just to be sure. Did you only give us a
partial mdp file?
Try adding this to your mdp file:
constraints = all-bonds
Hi Chris,
When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
set up the correct constraints. I've tested it and it conserves energy in
NVE. I run all he sims with constraints=all-bonds. I am now running a single
water box (800 water molecules) with 1s time steps and the volum
Hi Ilya,
If you did include the entire mdp file then you have a time step of 4
fs and no constraints (other than water). For a timestep of 2 fs, you
should constrain all-bonds (or some would say at least h-bonds) and
for 4 fs then you should also constrain angles involving hydrogens
(need
HI Chris,
On Tue, Apr 7, 2009 at 9:31 PM, wrote:
> Hi Ilya,
>
> First thing that comes to mind is that it is strange to couple a coulombic
> switching function with PME. While this could possibly be done correctly, I
> doubt that it is in fact done in the way that you expect (i.e. correctly) in
Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the s
Hi Ilya,
First thing that comes to mind is that it is strange to couple a
coulombic switching function with PME. While this could possibly be
done correctly, I doubt that it is in fact done in the way that you
expect (i.e. correctly) in gromacs. In fact, I think that grompp/mdrun
should p
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